Maybe you could fit some tubing into those drain holes and route that tubing into the bilge, even if it meant boring some holes in the storage compartment? Hopefully the tubing could be made to hug the sides of the storage box so it wouldn't be in the way and wouldn't get crushed.
A drawback is that tubing inserted into the drains obviously would be of much smaller inside diameter than the drains and would drain more slowly. Not so good in an emergency. Maybe there is a way to 4200 a section of pvc on the underside of the drain to allow for greater diameter tubing.
Not knowing the layout of your year Sailfish, I'm just throwing ideas out there. I wish I had a storage box under my mid-berth!